HEADER HYDROLASE 14-JUN-20 6ZDC TITLE STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN ENDO-ALPHA-MANNOSIDASE TITLE 2 MANEA IN COMPLEX WITH NICKEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOPROTEIN ENDO-ALPHA-1,2-MANNOSIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HENDO,MANDASELIN; COMPND 5 EC: 3.2.1.130; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MANEA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCOLD-I KEYWDS GOLGI, HYDROLASE, MANNOSIDASE, RETAINING EXPDTA X-RAY DIFFRACTION AUTHOR L.F.SOBALA,P.Z.FERNANDES,Z.HAKKI,A.J.THOMPSON,J.D.HOWE,M.HILL, AUTHOR 2 N.ZITZMANN,S.DAVIES,Z.STAMATAKI,T.D.BUTTERS,D.S.ALONZI,S.J.WILLIAMS, AUTHOR 3 G.J.DAVIES REVDAT 4 24-JAN-24 6ZDC 1 REMARK REVDAT 3 20-JAN-21 6ZDC 1 REMARK REVDAT 2 02-DEC-20 6ZDC 1 JRNL REVDAT 1 18-NOV-20 6ZDC 0 JRNL AUTH L.F.SOBALA,P.Z.FERNANDES,Z.HAKKI,A.J.THOMPSON,J.D.HOWE, JRNL AUTH 2 M.HILL,N.ZITZMANN,S.DAVIES,Z.STAMATAKI,T.D.BUTTERS, JRNL AUTH 3 D.S.ALONZI,S.J.WILLIAMS,G.J.DAVIES JRNL TITL STRUCTURE OF HUMAN ENDO-ALPHA-1,2-MANNOSIDASE (MANEA), AN JRNL TITL 2 ANTIVIRAL HOST-GLYCOSYLATION TARGET. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 29595 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 33154157 JRNL DOI 10.1073/PNAS.2013620117 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 21817 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.069 REMARK 3 FREE R VALUE TEST SET COUNT : 1106 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1231 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2877 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.73400 REMARK 3 B22 (A**2) : -2.64400 REMARK 3 B33 (A**2) : 3.37800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.249 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.199 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3007 ; 0.015 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2628 ; 0.035 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4097 ; 1.889 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6121 ; 2.341 ; 1.575 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 358 ; 6.494 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;34.041 ;21.916 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 480 ;15.072 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;14.786 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3371 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 684 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 634 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 59 ; 0.246 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1492 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 173 ; 0.141 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1408 ; 3.412 ; 5.002 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1407 ; 3.408 ; 4.998 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1759 ; 5.338 ; 7.478 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1760 ; 5.337 ; 7.482 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1598 ; 3.470 ; 5.195 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1599 ; 3.469 ; 5.198 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2333 ; 5.529 ; 7.678 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2334 ; 5.527 ; 7.681 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 6ZDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 1.4.1-GBA385BA-RELEASE REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21876 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 135.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.87200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.17 REMARK 200 STARTING MODEL: 5M17 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MIB BUFFER, PH 6.0. PROTEIN AT REMARK 280 5.5 MG/ML IN 50 MM POTASSIUM PHOSPHATE, 50 MM KCL. 150 NL REMARK 280 PROTEIN SOLUTION AND 150 NL RESERVOIR SOLUTION., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.26750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.95800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.26750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.95800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 80 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 81 REMARK 465 ASN A 82 REMARK 465 HIS A 83 REMARK 465 LYS A 84 REMARK 465 VAL A 85 REMARK 465 HIS A 86 REMARK 465 HIS A 87 REMARK 465 HIS A 88 REMARK 465 HIS A 89 REMARK 465 HIS A 90 REMARK 465 HIS A 91 REMARK 465 ILE A 92 REMARK 465 GLU A 93 REMARK 465 TRP A 131 REMARK 465 ASP A 132 REMARK 465 PRO A 133 REMARK 465 ARG A 134 REMARK 465 ILE A 135 REMARK 465 ALA A 136 REMARK 465 LYS A 137 REMARK 465 ASN A 138 REMARK 465 TYR A 139 REMARK 465 PRO A 140 REMARK 465 GLN A 141 REMARK 465 LEU A 455 REMARK 465 ASP A 456 REMARK 465 ARG A 457 REMARK 465 GLN A 458 REMARK 465 LEU A 459 REMARK 465 PRO A 460 REMARK 465 VAL A 461 REMARK 465 SER A 462 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 128 CG CD1 CD2 REMARK 470 ARG A 143 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 197 CG OD1 ND2 REMARK 470 LYS A 307 CE NZ REMARK 470 SER A 420 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 120 O HOH A 601 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 95 -71.31 -135.83 REMARK 500 ASN A 124 -168.33 -126.66 REMARK 500 PRO A 126 58.24 -63.26 REMARK 500 ASP A 149 73.56 -108.93 REMARK 500 ASP A 192 30.42 -93.27 REMARK 500 TYR A 323 -60.37 60.50 REMARK 500 ASN A 369 37.66 -92.32 REMARK 500 ILE A 377 58.94 33.26 REMARK 500 ASN A 403 48.20 -147.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 96 ND1 REMARK 620 2 HIS A 122 NE2 131.5 REMARK 620 3 HIS A 125 NE2 128.2 5.5 REMARK 620 4 HOH A 775 O 167.9 50.0 54.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 501 DBREF 6ZDC A 98 462 UNP Q5SRI9 MANEA_HUMAN 98 462 SEQADV 6ZDC MET A 81 UNP Q5SRI9 INITIATING METHIONINE SEQADV 6ZDC ASN A 82 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC HIS A 83 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC LYS A 84 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC VAL A 85 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC HIS A 86 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC HIS A 87 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC HIS A 88 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC HIS A 89 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC HIS A 90 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC HIS A 91 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC ILE A 92 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC GLU A 93 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC GLY A 94 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC ARG A 95 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC HIS A 96 UNP Q5SRI9 EXPRESSION TAG SEQADV 6ZDC MET A 97 UNP Q5SRI9 EXPRESSION TAG SEQRES 1 A 382 MET ASN HIS LYS VAL HIS HIS HIS HIS HIS HIS ILE GLU SEQRES 2 A 382 GLY ARG HIS MET PRO LEU ASN ASN TYR LEU HIS VAL PHE SEQRES 3 A 382 TYR TYR SER TRP TYR GLY ASN PRO GLN PHE ASP GLY LYS SEQRES 4 A 382 TYR ILE HIS TRP ASN HIS PRO VAL LEU GLU HIS TRP ASP SEQRES 5 A 382 PRO ARG ILE ALA LYS ASN TYR PRO GLN GLY ARG HIS ASN SEQRES 6 A 382 PRO PRO ASP ASP ILE GLY SER SER PHE TYR PRO GLU LEU SEQRES 7 A 382 GLY SER TYR SER SER ARG ASP PRO SER VAL ILE GLU THR SEQRES 8 A 382 HIS MET ARG GLN MET ARG SER ALA SER ILE GLY VAL LEU SEQRES 9 A 382 ALA LEU SER TRP TYR PRO PRO ASP VAL ASN ASP GLU ASN SEQRES 10 A 382 GLY GLU PRO THR ASP ASN LEU VAL PRO THR ILE LEU ASP SEQRES 11 A 382 LYS ALA HIS LYS TYR ASN LEU LYS VAL THR PHE HIS ILE SEQRES 12 A 382 GLU PRO TYR SER ASN ARG ASP ASP GLN ASN MET TYR LYS SEQRES 13 A 382 ASN VAL LYS TYR ILE ILE ASP LYS TYR GLY ASN HIS PRO SEQRES 14 A 382 ALA PHE TYR ARG TYR LYS THR LYS THR GLY ASN ALA LEU SEQRES 15 A 382 PRO MET PHE TYR VAL TYR ASP SER TYR ILE THR LYS PRO SEQRES 16 A 382 GLU LYS TRP ALA ASN LEU LEU THR THR SER GLY SER ARG SEQRES 17 A 382 SER ILE ARG ASN SER PRO TYR ASP GLY LEU PHE ILE ALA SEQRES 18 A 382 LEU LEU VAL GLU GLU LYS HIS LYS TYR ASP ILE LEU GLN SEQRES 19 A 382 SER GLY PHE ASP GLY ILE TYR THR TYR PHE ALA THR ASN SEQRES 20 A 382 GLY PHE THR TYR GLY SER SER HIS GLN ASN TRP ALA SER SEQRES 21 A 382 LEU LYS LEU PHE CYS ASP LYS TYR ASN LEU ILE PHE ILE SEQRES 22 A 382 PRO SER VAL GLY PRO GLY TYR ILE ASP THR SER ILE ARG SEQRES 23 A 382 PRO TRP ASN THR GLN ASN THR ARG ASN ARG ILE ASN GLY SEQRES 24 A 382 LYS TYR TYR GLU ILE GLY LEU SER ALA ALA LEU GLN THR SEQRES 25 A 382 ARG PRO SER LEU ILE SER ILE THR SER PHE ASN GLU TRP SEQRES 26 A 382 HIS GLU GLY THR GLN ILE GLU LYS ALA VAL PRO LYS ARG SEQRES 27 A 382 THR SER ASN THR VAL TYR LEU ASP TYR ARG PRO HIS LYS SEQRES 28 A 382 PRO GLY LEU TYR LEU GLU LEU THR ARG LYS TRP SER GLU SEQRES 29 A 382 LYS TYR SER LYS GLU ARG ALA THR TYR ALA LEU ASP ARG SEQRES 30 A 382 GLN LEU PRO VAL SER HET NI A 501 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *183(H2 O) HELIX 1 AA1 ASN A 113 GLY A 118 1 6 HELIX 2 AA2 ASP A 165 ALA A 179 1 15 HELIX 3 AA3 PRO A 200 ASN A 203 5 4 HELIX 4 AA4 LEU A 204 TYR A 215 1 12 HELIX 5 AA5 ASP A 230 GLY A 246 1 17 HELIX 6 AA6 ASP A 269 THR A 273 5 5 HELIX 7 AA7 LYS A 274 THR A 283 1 10 HELIX 8 AA8 LYS A 307 GLY A 316 1 10 HELIX 9 AA9 SER A 334 GLN A 336 5 3 HELIX 10 AB1 ASN A 337 TYR A 348 1 12 HELIX 11 AB2 ASN A 369 THR A 373 5 5 HELIX 12 AB3 ARG A 376 ASN A 378 5 3 HELIX 13 AB4 GLY A 379 GLN A 391 1 13 HELIX 14 AB5 GLY A 433 ALA A 451 1 19 SHEET 1 AA1 9 ILE A 351 ILE A 353 0 SHEET 2 AA1 9 GLY A 319 TYR A 321 1 N ILE A 320 O ILE A 353 SHEET 3 AA1 9 LEU A 298 LEU A 302 1 N ALA A 301 O TYR A 321 SHEET 4 AA1 9 MET A 264 VAL A 267 1 N PHE A 265 O ILE A 300 SHEET 5 AA1 9 LYS A 218 ILE A 223 1 N ILE A 223 O TYR A 266 SHEET 6 AA1 9 ILE A 181 TRP A 188 1 N LEU A 184 O LYS A 218 SHEET 7 AA1 9 ASN A 100 TYR A 107 1 N TYR A 107 O ALA A 185 SHEET 8 AA1 9 ILE A 397 ILE A 399 1 O ILE A 399 N PHE A 106 SHEET 9 AA1 9 SER A 355 VAL A 356 1 N VAL A 356 O SER A 398 SHEET 1 AA2 2 TYR A 254 LYS A 255 0 SHEET 2 AA2 2 ALA A 261 LEU A 262 -1 O LEU A 262 N TYR A 254 LINK ND1 HIS A 96 NI NI A 501 1555 1555 2.39 LINK NE2 HIS A 122 NI NI A 501 1555 1655 2.65 LINK NE2 HIS A 125 NI NI A 501 1555 1655 2.51 LINK NI NI A 501 O HOH A 775 1555 1455 2.68 CISPEP 1 PRO A 146 PRO A 147 0 0.62 CISPEP 2 THR A 400 SER A 401 0 8.08 CISPEP 3 ARG A 428 PRO A 429 0 6.33 SITE 1 AC1 5 HIS A 96 HIS A 122 HIS A 125 HOH A 709 SITE 2 AC1 5 HOH A 775 CRYST1 38.467 86.535 135.916 90.00 90.00 90.00 P 2 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.025996 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007357 0.00000